Open Access Highly Accessed Research article

The genome and transcriptome of the pine saprophyte Ophiostoma piceae, and a comparison with the bark beetle-associated pine pathogen Grosmannia clavigera

Sajeet Haridas1, Ye Wang1, Lynette Lim1, Sepideh Massoumi Alamouti1, Shaun Jackman2, Rod Docking2, Gordon Robertson2, Inanc Birol2, Jörg Bohlmann3 and Colette Breuil1*

Author Affiliations

1 Department of Wood Science, University of British Columbia, Vancouver, BC V6T1Z4, Canada

2 Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4E6, Canada

3 Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada

For all author emails, please log on.

BMC Genomics 2013, 14:373  doi:10.1186/1471-2164-14-373

Published: 2 June 2013

Additional files

Additional file 1:

Comparison of the genomes of O. piceae and G. clavigera, using MUMmer[57]. A dot plot genomic comparison showed no large scale synteny between the assembled genomes of O. piceae and G. clavigera. The genome of O. piceae is represented on the X-axis and that of G. clavigera on the Y-axis.

Format: PDF Size: 90KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

GO term enrichment in a set of 3,469 genes of O. piceae which were not reciprocal best blast hits in the G. clavigera genome. #Test represents the number of genes annotated with the respective GO term in the set of 3,469 genes and #Ref represents the number of genes with the GO classification in the entire O. piceae genome. P-value is calculated for Fisher’s exact test and FDR is the false discovery rate.

Format: XLS Size: 40KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

The eleven secondary metabolism clusters in O. piceae predicted by SMURF [34]. The backbone gene in each cluster is highlighted in yellow.

Format: XLSX Size: 22KB Download file

Open Data

Additional file 4:

Expression patterns of the 677 significantly differentially regulated genes. Expression values measured as FPKM (fragments per kilobase of exon per million fragments mapped). Genes that showed a 10 times or greater up-regulation in one condition or a related set of conditions are colour coded as described.

Format: XLS Size: 329KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Alternative splicing. To assess how important alternative splicing and transcripts were, we used Tophat and Cufflinks to map the RNA-seq reads to the genome assembly using the techniques described by Trapnell et al. The results suggested that approximately 150 alternative transcripts were expressed; however, all of these appeared to be false positives. The dominant cause of these false positive predictions was that closely spaced genes with overlapping UTRs were misassembled as single contigs, and differential regulation of such genes under different growth conditions appeared as alterative isoforms. In other cases, mapping errors produced false gene calls and alternative isoforms. These results indicated that alter415native splicing is not important under the growth conditions used for this study.

Format: DOC Size: 22KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 6:

Growth of O.piceae andG. clavigera on mannose, oleic acid and quinic acid. Fungal plugs were inoculated onto YNB plates (pH ~ 7, adjusted by KH2PO3-K2HPO3 buffer) containing a single carbon source; the plates with the fungus were incubated for 2 weeks. The growth of O. piceae is slower than G. clavigera, as shown with mannose. Control: YNB with no carbon.

Format: PDF Size: 1.6MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7:

Growth of O. piceae on MEA with or without the addition of monoterpenes for a week. A) Growth on MEA alone (arrow a: synemata and spores, arrow b: mycelium), B) Growth on MEA with monoterpenes, the mycelium was more aerial and fluffy (arrow c) while the production of asexual structures was highly inhibited.

Format: PDF Size: 909KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data